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I am trying to automate installation of miniconda and some packages thereafter within a singularity definition file to build an image. I am always getting the following error:

/.post.script: 10: conda: not found
FATAL:   While performing build: while running engine: exit status 127

Assuming that one has to restart shell after installing conda, is there any way to automate this? The definition file is written below.

Bootstrap: docker
From: ubuntu:22.04

%post
    apt-get update
    apt-get -y install gfortran
    apt-get -y install build-essential
    apt-get -y install manpages-dev
    apt-get -y install libgeos-dev
    apt-get -y install wget
    wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    /bin/bash Miniconda3-latest-Linux-x86_64.sh -bfp /opt
    conda update conda
    conda update python
    conda install pip -y
    pip install -y setuptools>=65.6
    pip install -y cartopy==0.21.0
    pip install -y contextily==1.2.0
    pip install -y fiona==1.8.21
    pip install -y pyproj==3.3.1
    pip install -y rtree==1.0.1
    pip install -y Shapely==1.8.2
    pip install -y numpy==1.23.0
    pip install -y pandas==1.4.3
    pip install -y geopandas==0.11.0
    pip install -y joblib==1.2.0
    pip install -y matplotlib==3.6.2
    pip install -y mercantile==1.2.1
    pip install -y pytest==7.2.0
    pip install -y python_dateutil==2.8.2
    pip install -y pytz==2021.3
    pip install -y timezonefinder==6.1.6
    pip install -y pyarrow==10.0.0
user106742
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    I suggest reading [this blog post](https://uwekorn.com/2021/03/01/deploying-conda-environments-in-docker-how-to-do-it-right.html). Define everything in a single YAML and let Mamba solve in one go, rather than doing iterative installations. – merv Nov 12 '22 at 15:01

0 Answers0